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When to rotate top box to bottom?

I am converting my equipment to 8 frame and yesterday while it was warm, I condensed a hive into the new equipment. I use one deep and one medium for brood boxes. What I noticed while I was doing this is that most of the deeps in the lower box where empty and more brood and bees were in the upper box. I realize this is a natural action for them during winter, but shouldn't I at some point rotate these boxes so the queen is in the lower box? When do I do this? Thanks.